Satu Koskinen

ON PHYLOGENY OF THE POLYTRICHALES

Phylogenetic analyses on Polytrichales were conducted using morphological characters as well as sequence data from the chloroplast genes rbcL and rps4 and the nuclear-encoded 18S rRNA gene. Our analyses included 22 species representing all genera of Polytrichales, plus eight outgroup species. Sequence data were obtained from 25, 22, and 19 taxa for 18S, rbcL and rps4 genes, respectively. Phylogenetic trees were constructed with parsimony analyses. Results lend support for recognition of Polytrichales as a distinct, monophyletic entity. After successively approximated weighting, Oedipodium griffithianum appears as the sister-group to Polytrichales. Within Polytrichales, Alophosia, Bartramiopsis, and Lyellia have the most basal placement outside a clade including all other genera. Atrichopsis, Dendroligotrichum, Itatiella, Meiotrichum, and Notoligotrichum are distinguished as a resolved monophyletic group while other genera are left as an unresolved entity. Resolution between these genera is achieved by successive weighting of data. After this, Dawsonia is resolved in the basal position within the clade and Polytrichastrum appears as a sister-taxon to Eopolytrichum and Polytrichum. Polytrichales are typically pioneer plants of open, sometimes even dry, habitats. Despite comprising only a small number of species, the order exhibits great diversity of shapes and sizes, from miniature plants such as Pogonatum piliferum (Dozy & Molk.) Touw of SE Asia and P. pensilvanicum (Hedw.) P. Beauv. of E North America to giants of Papua New Guinea like Dawsonia gigantea Geh. with stems reaching up to 80 cm. The most typical features of Polytrichales are the adaxial leaf lamellae and differentiation of leaves into a distinct blade and sheathing base. The hairy calyptra has given the group its name, although most genera have practically naked calyptrae. Sporophytes of Polytrichales normally have a well-developed peristome with at least 16 teeth that consist of whole cells. The epiphragm that covers the mouth of the capsule is a unique character that distinguishes most of the genera from all other groups of mosses. Size and shape of the urn vary greatly among genera (Schofield 1985; Smith 1971). The number of currently accepted genera in the Polytrichales is 19, and the approximate number of species in each genus is given in Table 1. One genus, along with its sole species Eopolytrichum antiquum Konopka, Herendeen, Merrill & Crane, is known only from beautifully preserved late Cretaceous fossils that reveal its structures in fine detail (Konopka et al. 1997). Many of the remaining genera are monotypic and all the others, with the exception of Pogonatum and Polytrichum, are fairly small. Schofield (1985) gives a conservative estimate of about 370 for the number of species in Polytrichales, but on the basis of recent critical revisions (e.g., Hyvinen 1989) it is realistic to assume that the number is actually closer to, or even less than, 200. Some species, like Polytrichum juniperinum Hedw., are almost cosmopolitan, while others, like the Macaronesian Alophosia azorica (Ren. & Card.) Card., are narrow endemics and possibly 1 This paper was presented at the 1997 Montr6al ABLS symposium sponsored by the Green Plant Phylogeny Research Coordination Group (with funding provided by DOE/NSF/USDA Panel on Collaborative Research in Plant Biology, USDA grant 94-7105-0713, Co-Pls Mark A. Buchheim, Brent D. Mishler, Russell L. Chapman). 0007-2745/98/489-504

In vivo recruitment analysis and a mutant strain without any group 2 σ factor reveal roles of different σ factors in cyanobacteria

1.75/0 This content downloaded from 207.46.13.162 on Fri, 01 Jul 2016 05:45:45 UTC All use subject to http://about.jstor.org/terms 490 THE BRYOLOGIST [VOL. 101 TABLE 1. The approximate number of species in the genera of Polytrichales. t-fossil. Alophosia 1 Meiotrichum 1 Atrichopsis 1 Notoligotrichum 10 Atrichum 15 Oligotrichum 10 Bartramiopsis 1 Pogonatum 50 Dawsonia 10 Polytrichadelphus 10 Dendroligotrichum 2 Polytrichastrum 10 t Eopolytrichum 1 Polytrichum 30 Hebantia 1 Psilopilum 2 Itatiella 1 Steereobryon 1 Lyellia 4 even threatened by extinction. Ecologically, the Polytrichales range from xerophytes like Polytrichum piliferum Hedw. to species of peaty, wet habitats like P. commune Hedw. Although their structure appears so obviously adapted to dry environments, the Polytrichales are largely absent from extremely arid regions, and the group exhibits greatest diversity in areas with humid or moist climates like SE Asia and Central America-northern South America. Phylogenetic relationships of the Polytrichales are particularly relevant to considerations of moss evolutionary history since the group is probably among the first of the lineages that diverged from the common ancestor of all mosses (Mishler & Churchill 1984). Smith (1971) presented a dendrogram with assumed phylogenetic trends for Polytrichales, and these ideas were further developed in his study of epiphragm structure and spore ornamentation (Smith 1974). Hyv6nen (1989), in a revision of Pogonatum that included cladistic analysis based on manual Hennigian argumentation, tentatively distinguished three entities in the Polytrichales as an unresolved basal trichotomy. These, and many other authors, viewed Polytrichastrum G. L. Sm. as the closest extant approximation to the common ancestor of Polytrichales. Forrest (1995) presented the first computer-aided analyses of Polytrichalean phylogeny based on a matrix of 50 characters compiled from the literature. The cladogram from her successively weighted analysis of these data is presented in Figure 1 (fig. 3b in Forrest 1995). In contrast to the views noted above, the position of Atrichum as sister to the remaining Polytrichales suggests that relatively simple members of the group more closely approximate the ancestral condition. This is congruent with ideas presented previously by Fleischer (1923). Forrests (1995) analyses resolved both strongly and weakly supported groups as implied by the number of characters supporting each clade. To test the strength of the phylogenetic hypotheses based on morphology and to determine whether they are congruent with other sources of data we explored Tetraphis

Endocytosis of Integrin-Binding Human Picornaviruses

In eubacteria, replacement of one σ factor in the RNA polymerase (RNAP) holoenzyme by another one changes the transcription pattern. Cyanobacteria are eubacteria characterized by oxygenic photosynthesis, and they typically encode numerous group 2 σ factors that closely resemble the essential primary σ factor. A mutant strain of the model cyanobacterium Synechocystis sp. PCC 6803 without functional group 2 σ factors (named as ΔsigBCDE) could not acclimate to heat, high salt or bright light stress, but in standard conditions ΔsigBCDE grew only 9% slower than the control strain. One‐fifth of the genes in ΔsigBCDE was differently expressed compared with the control strain in standard growth conditions and several physiological changes in photosynthesis, and pigment and lipid compositions were detected. To directly analyze the σ factor content of RNAP holoenzyme in vivo, a His‐tag was added to the γ subunit of RNAP in Synechocystis and RNAPs were collected. The results revealed that all group 2 σ factors were recruited by RNAP in standard conditions, but recruitment of SigB and SigC increased in heat stress, SigD in bright light, SigE in darkness and SigB, SigC and SigE in high salt, explaining the poor acclimation of ΔsigBCDE to these stress conditions.

Global biogeographic patterns in bipolar moss species

Picornaviruses that infect humans form one of the largest virus groups with almost three hundred virus types. They include significant enteroviral pathogens such as rhino-, polio-, echo-, and coxsackieviruses and human parechoviruses that cause wide range of disease symptoms. Despite the economic importance of picornaviruses, there are no antivirals. More than ten cellular receptors are known to participate in picornavirus infection, but experimental evidence of their role in cellular infection has been shown for only about twenty picornavirus types. Three enterovirus types and one parechovirus have experimentally been shown to bind and use integrin receptors in cellular infection. These include coxsackievirus A9 (CV-A9), echovirus 9, and human parechovirus 1 that are among the most common and epidemic human picornaviruses and bind to αV-integrins via RGD motif that resides on virus capsid. In contrast, echovirus 1 (E-1) has no RGD and uses integrin α2β1 as cellular receptor. Endocytosis of CV-A9 has recently been shown to occur via a novel Arf6- and dynamin-dependent pathways, while, contrary to collagen binding, E-1 binds inactive β1 integrin and enters via macropinocytosis. In this paper, we review what is known about receptors and endocytosis of integrin-binding human picornaviruses.

Genome Sequence of Coxsackievirus A6, Isolated during a Hand-Foot-and-Mouth Disease Outbreak in Finland in 2008

A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, yet its underlying mechanisms (vicariance or long-distance dispersal), origin and timing remain poorly understood. Here, combining a large-scale population dataset and multiple dating analyses, we examine the biogeography of four bipolar Polytrichales mosses, common to the Holarctic (temperate and polar Northern Hemisphere regions) and the Antarctic region (Antarctic, sub-Antarctic, southern South America) and other Southern Hemisphere (SH) regions. Our data reveal contrasting patterns, for three species were of Holarctic origin, with subsequent dispersal to the SH, while one, currently a particularly common species in the Holarctic (Polytrichum juniperinum), diversified in the Antarctic region and from here colonized both the Holarctic and other SH regions. Our findings suggest long-distance dispersal as the driver of bipolar disjunctions. We find such inter-hemispheric dispersals are rare, occurring on multi-million-year timescales. High-altitude tropical populations did not act as trans-equatorial ‘stepping-stones’, but rather were derived from later dispersal events. All arrivals to the Antarctic region occurred well before the Last Glacial Maximum and previous glaciations, suggesting that, despite the harsh climate during these past glacial maxima, plants have had a much longer presence in this southern region than previously thought.

The ω subunit of RNA polymerase is essential for thermal acclimation of the cyanobacterium Synechocystis sp. PCC 6803.

ABSTRACT Reports of hand-foot-and-mouth disease (HFMD) outbreaks caused by coxsackievirus A6 have increased worldwide after the report of the first outbreak in Finland in 2008. The complete genome of the first outbreak strain from a vesicle fluid specimen was determined.

Complete Genome Sequences of Three Strains of Coxsackievirus A7

The rpoZ gene encodes the small ω subunit of RNA polymerase. A ΔrpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions (constant illumination at 40 µmol photons m−2 s−1; 32°C; ambient CO2) but was heat sensitive and died at 40°C. In the control strain, 71 genes were at least two-fold up-regulated and 91 genes down-regulated after a 24-h treatment at 40°C, while in ΔrpoZ 394 genes responded to heat. Only 62 of these heat-responsive genes were similarly regulated in both strains, and 80% of heat-responsive genes were unique for ΔrpoZ. The RNA polymerase core and the primary σ factor SigA were down-regulated in the control strain at 40°C but not in ΔrpoZ. In accordance with reduced RNA polymerase content, the total RNA content of mild-heat-stress-treated cells was lower in the control strain than in ΔrpoZ. Light-saturated photosynthetic activity decreased more in ΔrpoZ than in the control strain upon mild heat stress. The amounts of photosystem II and rubisco decreased at 40°C in both strains while PSI and the phycobilisome antenna protein allophycocyanin remained at the same level as in standard conditions. The phycobilisome rod proteins, phycocyanins, diminished during the heat treatment in ΔrpoZ but not in the control strain, and the nblA1 and nblA2 genes (encode NblA proteins required for phycobilisome degradation) were up-regulated only in ΔrpoZ. Our results show that the ω subunit of RNAP is essential in heat stress because it is required for heat acclimation of diverse cellular processes.

Erratum to “Endocytosis of Integrin-Binding Human Picornaviruses”

ABSTRACT Genomes of three strains (Parker, USSR, and 275/58) of coxsackievirus A7 (CV-A7) were amplified by the long reverse transcription (RT)-PCR method and sequenced. While the sequences of Parker and USSR were identical, the similarities of 275/58 to the CV-A7 reference sequence, accession no. AY421765, were 82.6% and 96.2% for nucleotides and amino acids, respectively.

Inactivation of group 2 σ factors upregulates production of transcription and translation machineries in the cyanobacterium Synechocystis sp. PCC 6803

Due to unfortunate errors at the proof-reading stage, there are several misplaced references. A list of correct references in specified sentences is provided here as follows. Page 3: binding of E-1 to integrin α2β1 does not induce uncoating but instead may lead to the stabilization of capsid suggesting that viral RNA is released during endocytosis and not on plasma membrane [54, 60]. Page 3: this was based on the virus accumulation in caveolin-1-positive endosomes in SAOS cells overexpressing integrin α2β1 [60, 66]. However, at the same time and using another cell model, CV-1, the same authors demonstrated that majority of E-1 do not colocalize with caveolin-1 on the plasma membrane [67]. This observation was based on parallel comparisons to SV40, which is known to use caveolar route at least in some cell lines [62]. Page 4: dominant-negative caveolin-3 has been shown to block E-1 infection [68]. Page 4: which are localized in early endosomes and function in MVB formation [69]. Page 4: the recent finding that ESCRT complex recruits caveolin-1 into maturing intralumenal vesicles may explain why E-1 and caveolin-1 are found in similar structures early in infection [66, 69]. Page 5: we recently showed that CV-A9 internalization is dependent on β2-microglobulin [72]. Page 5: Arf6 (ADP-ribosylation factor 6) is a small GTPase, which has multiple roles in the regulation of membrane traffic and other cellular functions, but it was only recently when it was linked to virus endocytosis [72]. Page 5: and this may explain why it remains highly pathogenic [75, 76]. Page 5: which is evidently in contradiction with the suggestion that HPeV-1 is endocytosed via clathrin-mediated pathway [105]. On the other hand, MHC I (with β2M) has been linked to internalization of β1-integrins, but previously not shown to be involved in HPeV-1 infection [105]. Page 9: the data in reference [83] should be as follows: O. Heikkila, E. Karelehto, P. Merilahti et al., “HSPA5 protein (GRP78) and b2-microglobulin mediate internalization and entry of coxsackievirus A9 via a novel Arf6-dependent entry pathway in human epithelial colon adenocarcinoma cells,” Submitted.

Phylogeny of the Polytrichales (Bryophyta) based on simultaneous analysis of molecular and morphological data.

We show that the formation of the RNAP holoenzyme with the primary σ factor SigA increases in the ΔsigBCDE strain of the cyanobacterium Synechocystis sp. PCC 6803 lacking all group 2 σ factors. The high RNAP-SigA holoenzyme content directly induces transcription of a particular set of housekeeping genes, including ones encoding transcription and translation machineries. In accordance with upregulated transcripts, ΔsigBCDE contain more RNAPs and ribosomal subunits than the control strain. Extra RNAPs are fully active, and the RNA content of ΔsigBCDE cells is almost tripled compared to that in the control strain. Although ΔsigBCDE cells produce extra rRNAs and ribosomal proteins, functional extra ribosomes are not formed, and translation activity and protein content remained similar in ΔsigBCDE as in the control strain. The arrangement of the RNA polymerase core genes together with the ribosomal protein genes might play a role in the co-regulation of transcription and translation machineries. Sequence logos were constructed to compare promoters of those housekeeping genes that directly react to the RNAP-SigA holoenzyme content and those ones that do not. Cyanobacterial strains with engineered transcription and translation machineries might provide solutions for construction of highly efficient production platforms for biotechnical applications in the future.