29
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          ABSTRACT

          Intense biological conflicts between prokaryotic genomes and their genomic parasites have resulted in an arms race in terms of the molecular “weaponry” deployed on both sides. Using a recursive computational approach, we uncovered a remarkable class of multidomain proteins with 2 to 15 domains in the same polypeptide deployed by viruses and plasmids in such conflicts. Domain architectures and genomic contexts indicate that they are part of a widespread conflict strategy involving proteins injected into the host cell along with parasite DNA during the earliest phase of infection. Their unique feature is the combination of domains with highly disparate biochemical activities in the same polypeptide; accordingly, we term them polyvalent proteins. Of the 131 domains in polyvalent proteins, a large fraction are enzymatic domains predicted to modify proteins, target nucleic acids, alter nucleotide signaling/metabolism, and attack peptidoglycan or cytoskeletal components. They further contain nucleic acid-binding domains, virion structural domains, and 40 novel uncharacterized domains. Analysis of their architectural network reveals both pervasive common themes and specialized strategies for conjugative elements and plasmids or (pro)phages. The themes include likely processing of multidomain polypeptides by zincin-like metallopeptidases and mechanisms to counter restriction or CRISPR/Cas systems and jump-start transcription or replication. DNA-binding domains acquired by eukaryotes from such systems have been reused in XPC/RAD4-dependent DNA repair and mitochondrial genome replication in kinetoplastids. Characterization of the novel domains discovered here, such as RNases and peptidases, are likely to aid in the development of new reagents and elucidation of the spread of antibiotic resistance.

          IMPORTANCE This is the first report of the widespread presence of large proteins, termed polyvalent proteins, predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities combined in the same protein. While some of these domains are predicted to assist the invasive element in replication, transcription, or protection of their DNA, several are likely to target various host defense systems or modify the host to favor the parasite's life cycle. Notably, DNA-binding domains from these systems have been transferred to eukaryotes, where they have been incorporated into DNA repair and mitochondrial genome replication systems.

          Related collections

          Most cited references131

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Emergence of scaling in random networks

          Systems as diverse as genetic networks or the world wide web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This feature is found to be a consequence of the two generic mechanisms that networks expand continuously by the addition of new vertices, and new vertices attach preferentially to already well connected sites. A model based on these two ingredients reproduces the observed stationary scale-free distributions, indicating that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            A new generation of homology search tools based on probabilistic inference.

            Many theoretical advances have been made in applying probabilistic inference methods to improve the power of sequence homology searches, yet the BLAST suite of programs is still the workhorse for most of the field. The main reason for this is practical: BLAST's programs are about 100-fold faster than the fastest competing implementations of probabilistic inference methods. I describe recent work on the HMMER software suite for protein sequence analysis, which implements probabilistic inference using profile hidden Markov models. Our aim in HMMER3 is to achieve BLAST's speed while further improving the power of probabilistic inference based methods. HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm. Combined with efficient vector-parallel implementations on modern processors, these improvements synergize. HMMER3 uses more powerful log-odds likelihood scores (scores summed over alignment uncertainty, rather than scoring a single optimal alignment); it calculates accurate expectation values (E-values) for those scores without simulation using a generalization of Karlin/Altschul theory; it computes posterior distributions over the ensemble of possible alignments and returns posterior probabilities (confidences) in each aligned residue; and it does all this at an overall speed comparable to BLAST. The HMMER project aims to usher in a new generation of more powerful homology search tools based on probabilistic inference methods.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              (p)ppGpp: still magical?

              The fundamental details of how nutritional stress leads to elevating (p)ppGpp are questionable. By common usage, the meaning of the stringent response has evolved from the specific response to (p)ppGpp provoked by amino acid starvation to all responses caused by elevating (p)ppGpp by any means. Different responses have similar as well as dissimilar positive and negative effects on gene expression and metabolism. The different ways that different bacteria seem to exploit their capacities to form and respond to (p)ppGpp are already impressive despite an early stage of discovery. Apparently, (p)ppGpp can contribute to regulation of many aspects of microbial cell biology that are sensitive to changing nutrient availability: growth, adaptation, secondary metabolism, survival, persistence, cell division, motility, biofilms, development, competence, and virulence. Many basic questions still exist. This review tries to focus on some issues that linger even for the most widely characterized bacterial strains.
                Bookmark

                Author and article information

                Contributors
                Role: Editor
                Journal
                J Bacteriol
                J. Bacteriol
                jb
                jb
                JB
                Journal of Bacteriology
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                0021-9193
                1098-5530
                30 May 2017
                11 July 2017
                1 August 2017
                11 July 2017
                : 199
                : 15
                : e00245-17
                Affiliations
                [a ]National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
                [b ]Microbiology Department, Biomedical Sciences Institute, University of Sao Paulo, Cidade Universitária, São Paulo, Brazil
                University of Tennessee at Knoxville
                Author notes
                Address correspondence to L. Aravind, aravind@ 123456ncbi.nlm.nih.gov .

                Citation Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L. 2017. Polyvalent proteins, a pervasive theme in the intergenomic biological conflicts of bacteriophages and conjugative elements. J Bacteriol 199:e00245-17. https://doi.org/10.1128/JB.00245-17.

                Article
                00245-17
                10.1128/JB.00245-17
                5512222
                28559295
                7d633e08-dd63-4f96-bc9b-de0f3fcfd03d
                Copyright © 2017 Iyer et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 4 April 2017
                : 17 May 2017
                Page count
                Figures: 5, Tables: 0, Equations: 0, References: 168, Pages: 31, Words: 20154
                Funding
                Funded by: HHS | NIH | U.S. National Library of Medicine (NLM) https://doi.org/10.13039/100000092
                Award Recipient : L. Aravind
                Funded by: HHS | NIH | U.S. National Library of Medicine (NLM) https://doi.org/10.13039/100000092
                Award Recipient : Lakshminarayan M. Iyer
                Funded by: HHS | NIH | U.S. National Library of Medicine (NLM) https://doi.org/10.13039/100000092
                Award Recipient : A. M. Burroughs
                Funded by: HHS | NIH | U.S. National Library of Medicine (NLM) https://doi.org/10.13039/100000092
                Award Recipient : Swadha Anand
                Funded by: HHS | NIH | U.S. National Library of Medicine (NLM) https://doi.org/10.13039/100000092
                Award Recipient : Robson Francisco de Souza
                Categories
                Research Article
                Custom metadata
                August 2017

                Microbiology & Virology
                dna replication,dna-binding proteins,rnases,antirestriction,bacteriophages,biological conflicts,effectors,metallopeptidase,plasmids,transcription

                Comments

                Comment on this article