Journal articles: 'DUF3494'

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Bayer-Giraldi, Maddalena, Gen Sazaki, Ken Nagashima, Sepp Kipfstuhl, Dmitry A. Vorontsov, and Yoshinori Furukawa. "Growth suppression of ice crystal basal face in the presence of a moderate ice-binding protein does not confer hyperactivity." Proceedings of the National Academy of Sciences 115, no. 29 (July 2, 2018): 7479–84. http://dx.doi.org/10.1073/pnas.1807461115.

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Ice-binding proteins (IBPs) affect ice crystal growth by attaching to crystal faces. We present the effects on the growth of an ice single crystal caused by an ice-binding protein from the sea ice microalga Fragilariopsis cylindrus (fcIBP) that is characterized by the widespread domain of unknown function 3494 (DUF3494) and known to cause a moderate freezing point depression (below 1 °C). By the application of interferometry, bright-field microscopy, and fluorescence microscopy, we observed that the fcIBP attaches to the basal faces of ice crystals, thereby inhibiting their growth in the c direction and resulting in an increase in the effective supercooling with increasing fcIBP concentration. In addition, we observed that the fcIBP attaches to prism faces and inhibits their growth. In the event that the effective supercooling is small and crystals are faceted, this process causes an emergence of prism faces and suppresses crystal growth in the a direction. When the effective supercooling is large and ice crystals have developed into a dendritic shape, the suppression of prism face growth results in thinner dendrite branches, and growth in the a direction is accelerated due to enhanced latent heat dissipation. Our observations clearly indicate that the fcIBP occupies a separate position in the classification of IBPs due to the fact that it suppresses the growth of basal faces, despite its moderate freezing point depression.

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Lutz, Thomas, Kiersten Flodman, Alyssa Copelas, Honorata Czapinska, Megumu Mabuchi, Alexey Fomenkov, Xinyi He, Matthias Bochtler, and Shuang-yong Xu. "A protein architecture guided screen for modification dependent restriction endonucleases." Nucleic Acids Research 47, no. 18 (September 3, 2019): 9761–76. http://dx.doi.org/10.1093/nar/gkz755.

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Abstract Modification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or PD-(D/E)XK catalytic domain. The enzymes were clustered by similarity of their putative modification sensing domains into several groups. The TspA15I (VcaM4I, CmeDI), ScoA3IV (MsiJI, VcaCI) and YenY4I groups, all featuring a PUA superfamily domain, preferentially cleaved DNA containing 5-methylcytosine or 5-hydroxymethylcytosine. ScoA3V, also featuring a PUA superfamily domain, but of a different clade, exhibited 6-methyladenine stimulated nicking activity. With few exceptions, ORFs for PUA-superfamily domain containing endonucleases were not close to DNA methyltransferase ORFs, strongly supporting modification dependent activity of the endonucleases. DUF3427 domain containing fusion proteins had very little or no endonuclease activity, despite the presence of a putative PD-(D/E)XK catalytic domain. However, their expression potently restricted phage T4gt in Escherichia coli cells. In contrast to the ORFs for PUA domain containing endonucleases, the ORFs for DUF3427 fusion proteins were frequently found in defense islands, often also featuring DNA methyltransferases.

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Buchko, Garry W., Jan Abendroth, John I. Robinson, Isabelle Q. Phan, Peter J. Myler, and Thomas E. Edwards. "Structural diversity in the Mycobacteria DUF3349 superfamily." Protein Science 29, no. 3 (November 21, 2019): 670–85. http://dx.doi.org/10.1002/pro.3758.

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Reed, Colbie J., Geoffrey Hutinet, and Valérie de Crécy-Lagard. "Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase." Biomolecules 11, no. 9 (August 27, 2021): 1282. http://dx.doi.org/10.3390/biom11091282.

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Members of the DUF34 (domain of unknown function 34) family, also known as the NIF3 protein superfamily, are ubiquitous across superkingdoms. Proteins of this family have been widely annotated as “GTP cyclohydrolase I type 2” through electronic propagation based on one study. Here, the annotation status of this protein family was examined through a comprehensive literature review and integrative bioinformatic analyses that revealed varied pleiotropic associations and phenotypes. This analysis combined with functional complementation studies strongly challenges the current annotation and suggests that DUF34 family members may serve as metal ion insertases, chaperones, or metallocofactor maturases. This general molecular function could explain how DUF34 subgroups participate in highly diversified pathways such as cell differentiation, metal ion homeostasis, pathogen virulence, redox, and universal stress responses.

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Buchko, Garry W., Isabelle Phan, Peter J. Myler, Thomas C. Terwilliger, and Chang-Yub Kim. "Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c." Archives of Biochemistry and Biophysics 506, no. 2 (February 2011): 150–56. http://dx.doi.org/10.1016/j.abb.2010.12.001.

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Kuhn, Hunter W., Amanda G. Lasseter, Philip P. Adams, Carlos Flores Avile, Brandee L. Stone, Darrin R. Akins, Travis J. Jewett, and Mollie W. Jewett. "BB0562 is a nutritional virulence determinant with lipase activity important for Borrelia burgdorferi infection and survival in fatty acid deficient environments." PLOS Pathogens 17, no. 8 (August 20, 2021): e1009869. http://dx.doi.org/10.1371/journal.ppat.1009869.

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The Lyme disease spirochete Borrelia burgdorferi relies on uptake of essential nutrients from its host environments for survival and infection. Therefore, nutrient acquisition mechanisms constitute key virulence properties of the pathogen, yet these mechanisms remain largely unknown. In vivo expression technology applied to B. burgdorferi (BbIVET) during mammalian infection identified gene bb0562, which encodes a hypothetical protein comprised of a conserved domain of unknown function, DUF3996. DUF3996 is also found across adjacent encoded hypothetical proteins BB0563 and BB0564, suggesting the possibility that the three proteins could be functionally related. Deletion of bb0562, bb0563 and bb0564 individually and together demonstrated that bb0562 alone was important for optimal disseminated infection in immunocompetent and immunocompromised mice by needle inoculation and tick bite transmission. Moreover, bb0562 promoted spirochete survival during the blood dissemination phase of infection. Gene bb0562 was also found to be important for spirochete growth in low serum media and the growth defect of Δbb0562 B. burgdorferi was rescued with the addition of various long chain fatty acids, particularly oleic acid. In mammals, fatty acids are primarily stored in fat droplets in the form of triglycerides. Strikingly, addition of glyceryl trioleate, the triglyceride form of oleic acid, to the low serum media did not rescue the growth defect of the mutant, suggesting bb0562 may be important for the release of fatty acids from triglycerides. Therefore, we searched for and identified two canonical GXSXG lipase motifs within BB0562, despite the lack of homology to known bacterial lipases. Purified BB0562 demonstrated lipolytic activity dependent on the catalytic serine residues within the two motifs. In sum, we have established that bb0562 is a novel nutritional virulence determinant, encoding a lipase that contributes to fatty acid scavenge for spirochete survival in environments deficient in free fatty acids including the mammalian host.

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Zhang, Chenghua, Hong Huang, Wangqiu Deng, and Taihui Li. "Genome-Wide Analysis of the Zn(II)2Cys6 Zinc Cluster-Encoding Gene Family in Tolypocladium guangdongense and Its Light-Induced Expression." Genes 10, no. 3 (February 26, 2019): 179. http://dx.doi.org/10.3390/genes10030179.

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The Zn(II)2Cys6 zinc cluster gene family is a subclass of zinc-finger proteins, which are transcriptional regulators involved in a wide variety of biological processes in fungi. We performed genome-wide identification and characterization of Zn(II)2Cys6 zinc-cluster gene (C6 zinc gene) family in Tolypocladium guangdongense, Cordyceps militaris and Ophiocordyceps sinensis. Based on the structures of the C6 zinc domains, these proteins were observed to be evolutionarily conserved in ascomycete fungi. We focused on T. guangdongense, a medicinal fungus, and identified 139 C6 zinc genes which could be divided into three groups. Among them, 49.6% belonged to the fungal specific transcriptional factors, and 16% had a DUF3468 domain. Homologous and phylogenetic analysis indicated that 29 C6 zinc genes were possibly involved in the metabolic process, while five C6 zinc genes were supposed to be involved in asexual or sexual development. Gene expression analysis revealed that 54 C6 zinc genes were differentially expressed under light, including two genes that possibly influenced the development, and seven genes that possibly influenced the metabolic processes. This indicated that light may affect the development and metabolic processes, at least partially, through the regulation of C6 zinc genes in T. guangdongense. Our results provide comprehensive data for further analyzing the functions of the C6 zinc genes.

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Murakami, Yoshiko, Uamporn Siripanyaphinyo, Yeongjin Hong, Yuko Tashima, Yusuke Maeda, and Taroh Kinoshita. "The Initial Enzyme for Glycosylphosphatidylinositol Biosynthesis Requires PIG-Y, a Seventh Component." Molecular Biology of the Cell 16, no. 11 (November 2005): 5236–46. http://dx.doi.org/10.1091/mbc.e05-08-0743.

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Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by an unusually complex GPI-N-acetylglucosaminyltransferase (GPI-GnT) consisting of at least six proteins. Here, we report that human GPI-GnT requires another component, termed PIG-Y, a 71 amino acid protein with two transmembrane domains. The Burkitt lymphoma cell line Daudi, severely defective in the surface expression of GPI-anchored proteins, was a null mutant of PIG-Y. A complex of six components was formed without PIG-Y. PIG-Y appeared to be directly associated with PIG-A, implying that PIG-Y is the key molecule that regulates GPI-GnT activity by binding directly to the catalytic subunit PIG-A. PIG-Y is probably homologous to yeast Eri1p, a component of GPI-GnT. We did not obtain evidence for a functional linkage between GPI-GnT and ras GTPases in mammalian cells as has been reported for yeast cells. A single transcript encoded PIG-Y and, to its 5′ side, another protein PreY that has homologues in a wide range of organisms and is characterized by a conserved domain termed DUF343. These two proteins are translated from one mRNA by leaky scanning of the PreY initiation site.

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Jee, Samnyu, In-Jeong Kang, Gyeryeong Bak, Sera Kang, Jeongtae Lee, Sunggi Heu, and Ingyu Hwang. "Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing." Plant Pathology Journal 38, no. 1 (February 1, 2022): 12–24. http://dx.doi.org/10.5423/ppj.ft.09.2021.0147.

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In this study, we conducted whole-genome sequencing with six species of Pectobacterium composed of seven strains, JR1.1, BP201601.1, JK2.1, HNP201719, MYP201603, PZ1, and HC, for the analysis of pathogenic factors associated with the genome of Pectobacterium. The genome sizes ranged from 4,724,337 bp to 5,208,618 bp, with the GC content ranging from 50.4% to 52.3%. The average nucleotide identity was 98% among the two Pectobacterium species and ranged from 88% to 96% among the remaining six species. A similar distribution was observed in the carbohydrate-active enzymes (CAZymes) class and extracellular plant cell wall degrading enzymes (PCWDEs). HC showed the highest number of enzymes in CAZymes and the lowest number in the extracellular PCWDEs. Six strains showed four subsets, and HC demonstrated three subsets, except hasDEF, in type I secretion system, while the type II secretion system of the seven strains was conserved. Components of human pathogens, such as Salmonella pathogenicity island 1 type type III secretion system (T3SS) and effectors, were identified in PZ1; T3SSa was not identified in HC. Two putative effectors, including hrpK, were identified in seven strains along with dspEF. We also identified 13 structural genes, six regulator genes, and five accessory genes in the type VI secretion system (T6SS) gene cluster of six Pectobacterium species, along with the loss of T6SS in PZ1. HC had two subsets, and JK2.1 had three subsets of T6SS. With the GxSxG motif, the phospholipase A gene did locate among tssID and duf4123 genes in the T6SSa cluster of all strains. Important domains were identified in the vgrG/paar islands, including duf4123, duf2235, vrr-nuc, and duf3396.

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Sexton, Danielle L., Renée J. St-Onge, Henry J. Haiser, Mary R. Yousef, Lauren Brady, Chan Gao, Jacqueline Leonard, and Marie A. Elliot. "Resuscitation-Promoting Factors Are Cell Wall-Lytic Enzymes with Important Roles in the Germination and Growth of Streptomyces coelicolor." Journal of Bacteriology 197, no. 5 (December 15, 2014): 848–60. http://dx.doi.org/10.1128/jb.02464-14.

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Dormancy is a common strategy adopted by bacterial cells as a means of surviving adverse environmental conditions. ForStreptomycesbacteria, this involves developing chains of dormant exospores that extend away from the colony surface. Both spore formation and subsequent spore germination are tightly controlled processes, and while significant progress has been made in understanding the underlying regulatory and enzymatic bases for these, there are still significant gaps in our understanding. One class of proteins with a potential role in spore-associated processes are the so-called resuscitation-promoting factors, or Rpfs, which in other actinobacteria are needed to restore active growth to dormant cell populations. The model speciesStreptomyces coelicolorencodes five Rpf proteins (RpfA to RfpE), and here we show that these proteins have overlapping functions during growth. Collectively, theS. coelicolorRpfs promote spore germination and are critical for growth under nutrient-limiting conditions. Previous studies have revealed structural similarities between the Rpf domain and lysozyme, and ourin vitrobiochemical assays revealed various levels of peptidoglycan cleavage capabilities for each of these fiveStreptomycesenzymes. Peptidoglycan remodeling by enzymes such as these must be stringently governed so as to retain the structural integrity of the cell wall. Our results suggest that one of the Rpfs, RpfB, is subject to a unique mode of enzymatic autoregulation, mediated by a domain of previously unknown function (DUF348) located within the N terminus of the protein; removal of this domain led to significantly enhanced peptidoglycan cleavage.

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Miller, Mitchell D., L. Aravind, Constantina Bakolitsa, Christopher L. Rife, Dennis Carlton, Polat Abdubek, Tamara Astakhova, et al. "Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation." Acta Crystallographica Section F Structural Biology and Crystallization Communications 66, no. 10 (July 6, 2010): 1167–73. http://dx.doi.org/10.1107/s1744309110007517.

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Raymond, James A., Michael G. Janech, and Marco Mangiagalli. "Ice-Binding Proteins Associated with an Antarctic Cyanobacterium, Nostoc sp. HG1." Applied and Environmental Microbiology 87, no. 2 (November 6, 2020). http://dx.doi.org/10.1128/aem.02499-20.

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ABSTRACT Ice-binding proteins (IBPs) have been identified in numerous polar algae and bacteria, but so far not in any cyanobacteria, despite the abundance of cyanobacteria in polar regions. We previously reported strong IBP activity associated with an Antarctic Nostoc species. In this study, to identify the proteins responsible, as well as elucidate their origin, we sequenced the DNA of an environmental sample of this species, designated Nostoc sp. HG1, and its bacterial community and attempted to identify IBPs by looking for known IBPs in the metagenome and by looking for novel IBPs by tandem mass spectrometry (MS/MS) proteomics analyses of ice affinity-purified proteins. The metagenome contained over 116 DUF3494-type IBP genes, the most common type of IBP identified so far. One of the IBPs could be confidently assigned to Nostoc, while the others could be attributed to diverse bacteria, which, surprisingly, accounted for the great majority of the metagenome. Recombinant Nostoc IBPs (nIBPs) had strong ice-structuring activities, and their circular dichroism spectra were consistent with the secondary structure of a DUF3494-type IBP. nIBP is unusual in that it is the only IBP identified so far to have a PEP (amino acid motif) C-terminal signal, a signal that has been associated with anchoring to the outer cell membrane. These results suggest that the observed IBP activity of Nostoc sp. HG1 was due to a combination of endogenous and exogenous IBPs. Amino acid and nucleotide sequence analyses of nIBP raise the possibility that it was acquired from a planctomycete. IMPORTANCE The horizontal transfer of genes encoding ice-binding proteins (IBPs), proteins that confer freeze-thaw tolerance, has allowed many microorganisms to expand their ranges into polar regions. One group of microorganisms for which nothing is known about its IBPs is cyanobacteria. In this study, we identified a cyanobacterial IBP and showed that it was likely acquired from another bacterium, probably a planctomycete. We also showed that a consortium of IBP-producing bacteria living with the Nostoc contribute to its IBP activity.

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Hespanhol, Julia Takuno, Daniel Enrique Sanchez-Limache, Gianlucca Gonçalves Nicastro, Liam Mead, Edgar Enrique Llontop, Gustavo Chagas-Santos, Chuck Shaker Farah, et al. "Antibacterial T6SS effectors with a VRR-Nuc domain are structure-specific nucleases." eLife 11 (October 13, 2022). http://dx.doi.org/10.7554/elife.82437.

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The type VI secretion system (T6SS) secretes antibacterial effectors into target competitors. Salmonella spp. encode five phylogenetically distinct T6SSs. Here we characterize the function of the SPI-22 T6SS of Salmonella bongori showing that it has antibacterial activity and identify a group of antibacterial T6SS effectors (TseV1-4) containing an N-terminal PAAR-like domain and a C-terminal VRR-Nuc domain encoded next to cognate immunity proteins with a DUF3396 domain (TsiV1-4). TseV2 and TseV3 are toxic when expressed in Escherichia coli and bacterial competition assays confirm that TseV2 and TseV3 are secreted by the SPI-22 T6SS. Phylogenetic analysis reveals that TseV1-4 are evolutionarily related to enzymes involved in DNA repair. TseV3 recognizes specific DNA structures and preferentially cleave splayed arms, generating DNA double-strand breaks and inducing the SOS response in target cells. The crystal structure of the TseV3:TsiV3 complex reveals that the immunity protein likely blocks the effector interaction with the DNA substrate. These results expand our knowledge on the function of Salmonella pathogenicity islands, the evolution of toxins used in biological conflicts, and the endogenous mechanisms regulating the activity of these toxins.

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Santamaría, Ramón I., Laura Sevillano, Jesús Martín, Olga Genilloud, Ignacio González, and Margarita Díaz. "The XRE-DUF397 Protein Pair, Scr1 and Scr2, Acts as a Strong Positive Regulator of Antibiotic Production in Streptomyces." Frontiers in Microbiology 9 (November 16, 2018). http://dx.doi.org/10.3389/fmicb.2018.02791.

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Guilhen, Cyril, Wanessa C. Lima, Estelle Ifrid, Xenia Crespo-Yañez, Otmane Lamrabet, and Pierre Cosson. "A New Family of Bacteriolytic Proteins in Dictyostelium discoideum." Frontiers in Cellular and Infection Microbiology 10 (February 3, 2021). http://dx.doi.org/10.3389/fcimb.2020.617310.

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Phagocytic cells ingest and destroy bacteria efficiently and in doing so ensure the defense of the human body against infections. Phagocytic Dictyostelium discoideum amoebae represent a powerful model system to study the intracellular mechanisms ensuring destruction of ingested bacteria in phagosomes. Here, we discovered the presence of a bacteriolytic activity against Klebsiella pneumoniae in cellular extracts from D. discoideum. The bacteriolytic activity was detected only at a very acidic pH mimicking the conditions found in D. discoideum phagosomes. It was also strongly decreased in extracts of kil1 KO cells that were previously described to kill inefficiently internalized bacteria, suggesting that the activity observed in vitro is involved in killing of bacteria in phagosomes. We purified a fraction enriched in bacteriolytic activity where only 16 proteins were detected and focused on four proteins selectively enriched in this fraction. Three of them belong to a poorly characterized family of D. discoideum proteins exhibiting a DUF3430 domain of unknown function and were named BadA (Bacteriolytic D. discoideum A), BadB, and BadC. We overexpressed the BadA protein in cells, and the bacteriolytic activity increased concomitantly in cell extracts. Conversely, depletion of BadA from cell extracts decreased significantly their bacteriolytic activity. Finally, in cells overexpressing BadA, bacterial killing was faster than in parental cells. Together these results identify BadA as a D. discoideum protein required for cellular bactericidal activity. They also define a new strategy to identify and characterize bactericidal proteins in D. discoideum cells.

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Journal articles on the topic 'DUF3494'

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