The Flexible Genome of Acidophilic Prokaryotes.

Simon Beard,Douglas E Rawlings,Raquel Quatrini,Francisco J Ossandon

doi:10.21775/cimb.040.231

Abstract

Over the last couple of decades there has been considerable progress in the identification and understanding of the mobile genetic elements that are exchanged between microbes in extremely acidic environments, and of the genes piggybacking on them. Numerous plasmid families, unique viruses of bizarre morphologies and lyfe cycles, as well as plasmid-virus chimeras, have been isolated from acidophiles and characterized to varying degrees. Growing evidence provided by omic-studies have shown that the mobile elements repertoire is not restricted to plasmids and viruses, but that a plethora of integrative elements ranging from miniature inverted repeat transposable elements to large integrative conjugative elements populate the genomes of acidophilic bacteria and archaea. This article reviews the diversity of elements that have been found to constitute the flexible genome of acidophiles. Special emphasis is put on the knowledge generated for Sulfolobus (archaea) and species of the bacterial genera Acidithiobacillus and Leptospirillum. Also, recent knowledge on the strategies used by acidophiles to contain deletereous exchanges while allowing innovation, and the emerging details of the molecular biology of these systems, are discussed. Major lacunae in our understanding of the mobilome of acidophilic prokaryotes and topics for further investigations are identified.

Highlights

Bacteria and archaea have evolved efficient genome modification mechanisms that allow them to adapt rapidly and effectively to ever-changing environmental conditions and to colonize a plethora of ecological niches
Thermoplasma acidophilum and Picrophilus torridus share approximately the same fraction of genes (65% of their proteomes) between them, as they do with Sulfolobus solfataricus, a very distant relative that often inhabits the same environment, whereas only 35% of their genes are present in Pyrococcus furiosus, a closer relative (Fütterer et al, 2004)
The best-characterized plasmids are the pKEF family plasmids. They range in size between 20 and 40 Kb and are all medium copy number plasmids in S. solfataricus test strain PH1 (20 to 40 copies/chromosome); slightly lower copy numbers occur in their natural hosts (Prangishvili et al, 1998)

Summary

Introduction

Bacteria and archaea have evolved efficient genome modification mechanisms that allow them to adapt rapidly and effectively to ever-changing environmental conditions and to colonize a plethora of ecological niches. They range in size between 20 and 40 Kb and are all medium copy number plasmids in S. solfataricus test strain PH1 (20 to 40 copies/chromosome); slightly lower copy numbers occur in their natural hosts (Prangishvili et al, 1998) Conserved genes within this family are organized in three functionally distinct genomic sections grouping the conjugation genes, the origin of replication and the proposed replication genes which resemble pRN family plasmids repA, copG and plrA genes (Greve et al, 2004). One of the well-conserved regions of pKEF plasmids has provided hints in this respect This region contains six ORFs predicted to encode the core conjugative apparatus in Sulfolobus, and two of these genes products (pKEF9: p12 and p01) exhibit sequence motifs and domain structures characteristic of the bacterial Type IV secretion system coupling protein (VirD4/ T4CP) and relaxase (VirB4) proteins required for DNA transfer.

40.4 Nonlytic

Findings

III IV