https://repository.kopri.re.kr/handle/201206/5525 2026-04-07T09:31:24Z 2026-04-07T09:31:24Z Kim, Kyung Mo Kim, Byung Kwon Arshan Nasir Choe, Hanna https://repository.kopri.re.kr/handle/201206/6285 2022-03-24T07:11:26Z 2017-01-01T00:00:00Z

Title: Complete genome of a metabolically-diverse marine bacterium Shewanella japonica KCTC 22435T Authors: Kim, Kyung Mo; Kim, Byung Kwon; Arshan Nasir; Choe, Hanna Abstract: Shewanella japonica KCTC 22435T is a facultatively anaerobic, Gram-negative, mesophilic, rod-shaped bacterium isolated from sea water at the Pacific Institute of Bio-organic Chemistry of the Marine Experimental Station, Troitza Bay, Gulf of Peter the Great, Russia. Here, we report the complete genome of S. japonica KCTC 22435T, which consists of 4,975,677 bp (G + C content of 40.80%) with a single chromosome, 4036 protein-coding genes, 97 tRNAs and 8 rRNA operons. Genes detected in the genome reveal that the strain possesses a type II secretion system, cytochrome c family proteins with various numbers of heme-binding motifs, and metabolic pathways for utilizing diverse carbon sources, supporting the potential of KCTC 22435T to generate electricity in salinity culture conditions.

2017-01-01T00:00:00Z Arshan Nasir Gustavo Caetano-Anolles Kim, Kyung Mo https://repository.kopri.re.kr/handle/201206/6511 2022-03-24T07:12:28Z 2017-01-01T00:00:00Z

Title: Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells Authors: Arshan Nasir; Gustavo Caetano-Anolles; Kim, Kyung Mo Abstract: Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors. However, it was recently argued that the rooting of our trees and the basal placement of viruses was artifactually induced by small genome (proteome) size. Here we show that these claims arise from misunderstanding and misinterpretations of cladistic methodology. Trees are reconstructed unrooted, and thus, their topologies cannot be distorted a posteriori by the rooting methodology. Tracing proteome size in trees and multidimensional views of evolutionary relationships as well as tests of leaf stability and exclusion/inclusion of taxa demonstrated that the smallest proteomes were neither attracted toward the root nor caused any topological distortions of the trees. Simulations confirmed that taxa clustering patterns were independent of proteome size and were determined by the presence of known evolutionary relatives in data matrices, highlighting the need for broader taxon sampling in phylogeny reconstruction. Instead, phylogenetic tracings of proteome size revealed a slowdown in innovation of the structural domain vocabulary and four regimes of allometric scaling that reflected a Heaps law. These regimes explained increasing economies of scale in the evolutionary growth and accretion of kernel proteome repertoires of viruses and cellular organisms that resemble growth of human languages with limited vocabulary sizes. Results reconcile dynamic and static views of domain frequency distributions that are consistent with the axiom of spatiotemporal continuity that is tenet of evolutionary thinking.

2017-01-01T00:00:00Z SS Malik Arshan Nasir Gustavo Caetano-Anolles Kim, Kyung Mo S Azem-e-Zahra https://repository.kopri.re.kr/handle/201206/6512 2022-03-24T07:12:28Z 2017-01-01T00:00:00Z

Title: Do Viruses Exchange Genes across Superkingdoms of Life? Authors: SS Malik; Arshan Nasir; Gustavo Caetano-Anolles; Kim, Kyung Mo; S Azem-e-Zahra Abstract: Viruses can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells. Such interactions create opportunities for genetic exchange between viruses and organisms of non-host superkingdoms. Here, we take an atypical approach to revisit virus-cell interactions by first identifying protein fold structures in the proteomes of archaeoviruses, bacterioviruses, and eukaryoviruses and second by tracing their spread in the proteomes of superkingdoms Archaea, Bacteria, and Eukarya. The exercise quantified protein structural homologies between viruses and organisms of their host and non-host superkingdoms and revealed likely candidates for virus-to-cell and cell-to-virus gene transfers. Unexpected lifestyle-driven genetic affiliations between bacterioviruses and Eukarya and eukaryoviruses and Bacteria were also predicted in addition to a large cohort of protein folds that were universally shared by viral and cellular proteomes and virus-specific protein folds not detected in cellular proteomes. These protein folds provide unique insights into viral origins and evolution that are generally difficult to recover with traditional sequence alignment-dependent evolutionary analyses owing to the fast mutation rates of viral gene sequences.

2017-01-01T00:00:00Z