Linear Plasmids in Filamentous Fungi

Among the filamentous fungi, a great number of plasmids have been described for both ascomycetes and basidiomycetes; almost all of them reside in mitochondria (reviewed by Griffiths 1995). The only known exceptions are the linear plasmids from Alternaria alternata, which are apparently not localized in mitochondria (Shepherd 1992). Though there are circular plasmids, such as Mauriceville, Fiji, and LaBelle plasmids in Neurospora (Griffiths 1995), the great majority are linear molecules with TPs and TIRs. Frequencies of linear plasmids have been determined for a number of fungi belonging to different genera, such as Neurospora, Claviceps, Fusarium, Blumeria, Epichloë, and Podospora (Arganoza et al. 1994; Samac and Leong 1988; Morgen et al. 1991; van der Gaag et al. 1998; Giese et al. 1990; Tudzynski et al. 1983; Tudzyn-ski and Esser 1986; Düvell et al. 1988). Overall frequencies were estimated to match approximately 8-16% (van der Gaag et al. 1998); however, when the geographic distribution was taken into consideration, it became evident that linear plasmids may be endemic to specific geographic regions, in which they represent the norm rather than an exception. The kalilo plasmid may serve

Table 1 Mitochondrial linear plasmids of filamentous fungi for which complete nucleotide sequences are available (GenBank accession numbers in parentheses). Sizes of plasmids and TIRs are indicated. Coding capacity specifies genes identified; accession numbers for deduced polypeptides are indicated along with their sizes in amino acids (aa). DP, RP: DNA polymerase and RNA polymerase genes; unknown: gene of unknown function

Table 1 Mitochondrial linear plasmids of filamentous fungi for which complete nucleotide sequences are available (GenBank accession numbers in parentheses). Sizes of plasmids and TIRs are indicated. Coding capacity specifies genes identified; accession numbers for deduced polypeptides are indicated along with their sizes in amino acids (aa). DP, RP: DNA polymerase and RNA polymerase genes; unknown: gene of unknown function

Species

Plasmid

Size/

Coding capacity

Refs.

(acc. no.)

TIRs (bp) (size, acc. no.)

Pleurotus

pMLP1

9879

unknown (239 aa; AAD39925)

Kim et al.

ostreatus

(AF126285)

381

RP (903 aa; AAD39926)

(2000)

DP (1346 aa; AAD39927)

Neurospora

maranhar

7052

RP (896 aa; CAA39045)

Court and

crassa

(X55361)

349

DP (1021 aa; CAA39046)

Bertrand (1992)

Neurospora

harbin-3

7050

RP (896 aa; AAD31445)

Xu et al. (1999)

intermedia

(NC_000843)

350

DP (1035 aa; AAD31446)

kalilo

8642

RP (811 aa; CAA36326)

Chan et al.

(X52106)

1365

DP (893 aa; CAA36327)

(1991b)

Gelasinospora

Gel-kal

8231

RP (987 aa; AAB41447)

Yuewang et al.

sp.

(L40494)

1137

DP (831 aa; AAB41448)

(1996)

Blumeria

pBgh

7965

RP (973 aa; AAO37818)

Giese et al.

graminis

(AY189817)

610

DP (1062 aa; AAO37819)

(2003)

Morchella

pMC3-2

6044

unknown (306 aa; CAB52198)

Rohe et al.

conica

(X63909)

720

DP (901 aa; CAA45364)

(1991)

Podospora

pAL2-1

8395

RP (948 aa; CAA43116)

Hermanns and

anserina

(X60707)

975

DP (1197 aa; CAA43117)

Osiewacz

(1992)

Claviceps

pClKl

6752

RP (970 aa; Nt. 112-3021)

Oeser and

purpurea

(X15648)

327

DP (1097 aa; Nt. 6641-3351)

Tudzynski

4 minor ORFs

(1989)

pClT5

7113

RP (947 aa; Nt. 356-3199)

Oeser et al.

(X68490)

574

DP (1050 aa; Nt. 6758-3606)

(1993)

5 minor ORFs

Ascobolus

pAI1

5142

DP (1202 aa; CAA34106)

Kempken et al.

immersus

(X15982)

535

4 minor ORFs

(1989)

as an example, as it was found routinely in isolates from Hawaii (Yang and Griffiths 1993; Maas et al. 2005), but less frequently in Asia, Africa, Central America, and South Pacific islands (Arganoza et al. 1994). In Claviceps purpurea and Blumeria graminis, linear plasmids occur frequently irrespective of their geographic origins (Tudzynski and Esser 1986; Düvell et al. 1988; Giese et al. 1990, 2003), being indicative of a widespread distribution in these fungi.

Partial or entire nucleotide sequences are available for a considerable number of linear plasmids from both filamentous ascomycetes and basidiomycetes (Table 1). Sizes vary from 5142 bp (pAI1 of Ascobolus immersus) to 9879 bp (pMLP1 of Pleurotus ostreatus); all of them possess TIRs ranging in size from 327 to 1365 bp (Table 1).

Most known linear plasmids from filamentous fungi display a rather common genetic organization as for the maranhar plasmid from Neurospora crassa (Fig. 2), which contains two ORFs in an inverse orientation encoding the TP-DNA polymerase and the RNA polymerase, respectively. However, differently organized plasmids exist as well, such as pAI1 of A. immersus and pMC3-2 of the morel, which encode the typical TP-DNA polymerase fusion gene but lack an RNA polymerase gene (Kempken et al. 1989; Rohe et al. 1991; Fig. 2). In both instances the plasmids concomitantly exist along with other elements, suggesting the RNA polymerase to be encoded by an accompanying plasmid.

Such a scenario has indeed been proven for the linear plasmids discovered first, i.e., the S plasmids S1 and S2 from maize (Levings and Sederoff 1983; Paillard et al. 1985); S1 encodes the TP and DNA polymerase, while the RNA polymerase gene is located on S2.

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